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Semantic integration and analysis of clinical data [article]

Hong Sun, Kristof Depraetere, Jos De Roo, Boris De Vloed, Giovanni Mels, Dirk Colaert
<span title="2012-10-24">2012</span> <i > arXiv </i> &nbsp; <span class="release-stage" >pre-print</span>
There is a growing need to semantically process and integrate clinical data from different sources for Clinical Data Management and Clinical Decision Support in the healthcare IT industry.  ...  The resulting data expressed in domain formalisms can be integrated and analyzed, though originating from very distinct sources.  ...  Acknowledgement This research has been supported by the EU-IST-FP7 DebugIT project and the HIT4CLL project.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener" href="https://arxiv.org/abs/1210.4405v2">arXiv:1210.4405v2</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/f4llngb33rbazaaxli34urlzo4">fatcat:f4llngb33rbazaaxli34urlzo4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200914055529/https://arxiv.org/ftp/arxiv/papers/1210/1210.4405.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/c0/7f/c07f98bfca7a0776e5e88c09a559dd8775e0aba1.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener" href="https://arxiv.org/abs/1210.4405v2" title="arxiv.org access"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> arxiv.org </button> </a>

Towards a Semantic Data Harmonization Federated Infrastructure [chapter]

Catalina Martinez-Costa, Francisco Abad-Navarro
<span title="2021-05-27">2021</span> <i title="IOS Press"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/4ju2ftoebbcvrjj6lqnnbh42wq" style="color: black;">Studies in Health Technology and Informatics</a> </i> &nbsp;
This common data model integrates content from well-known biomedical ontologies like SNOMED CT by using the BTL2 upper level ontology, and is imported into a graph database.  ...  We successfully integrated three datasets and made some test queries showing the feasibility of the approach.  ...  Ontology harmonization infrastructure. In the middle the semantic CDM that uses BTL2 to integrate clinical and information entities [12] .  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3233/shti210116">doi:10.3233/shti210116</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/34042701">pmid:34042701</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/jxttu4mqc5a5bjgqrtszlav5ku">fatcat:jxttu4mqc5a5bjgqrtszlav5ku</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210715151809/https://ebooks.iospress.nl/pdf/doi/10.3233/SHTI210116" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/ca/03/ca03619f05e10c5df3a123ad02a9218891cdc5f7.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3233/shti210116"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> Publisher / doi.org </button> </a>

Unlocking Data for Clinical Research – The German i2b2 Experience

S. Mate, K Helbing, U. Sax, H.U. Prokosch, T. Ganslandt
<span title="">2011</span> <i title="Schattauer GmbH"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/kmly2oujtfb67pwdjaqxmsj7am" style="color: black;">Applied Clinical Informatics</a> </i> &nbsp;
The i2b2 platform has been introduced in some US research communities as a tool for data integration and querying by clinical users.  ...  Methods: A set of four research usage scenarios was chosen, including the transformation and import of ontology and fact data from existing clinical data collections into i2b2 v1.4 instances.  ...  integration of clinical and research data [4, 5] .  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.4338/aci-2010-09-cr-0051">doi:10.4338/aci-2010-09-cr-0051</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/23616864">pmid:23616864</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3631913/">pmcid:PMC3631913</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/xziannsm2jf53cupmftjamu3v4">fatcat:xziannsm2jf53cupmftjamu3v4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200209064406/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC3631913&amp;blobtype=pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/c7/30/c73003f8d7016dac2b372cb86d0329f5dfede18f.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.4338/aci-2010-09-cr-0051"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3631913" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Applications of the ACGT Master Ontology on Cancer [chapter]

Mathias Brochhausen, Gabriele Weiler, Luis Martín, Cristian Cocos, Holger Stenzhorn, Norbert Graf, Martin Dörr, Manolis Tsiknakis, Barry Smith
<span title="">2008</span> <i title="Springer Berlin Heidelberg"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/2w3awgokqne6te4nvlofavy5a4" style="color: black;">Lecture Notes in Computer Science</a> </i> &nbsp;
both clinical and molecular data.  ...  In this paper we present applications of the ACGT Master Ontology (MO) which is a new terminology resource for a transnational network providing data exchange in oncology, emphasizing the integration of  ...  A model for integrating that data must include this aspect.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/978-3-540-88875-8_132">doi:10.1007/978-3-540-88875-8_132</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/wuovugba2rdxdkfflrxohgxprm">fatcat:wuovugba2rdxdkfflrxohgxprm</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20100612022550/http://ontology.buffalo.edu/medo/ACGT.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/b8/1b/b81bc2113d31509d2b4d25c4a6aee567d9ea5670.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/978-3-540-88875-8_132"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> springer.com </button> </a>

Role of semantic web in health informatics

Satya S. Sahoo, Amit Sheth, Guo-Qiang Zhang
<span title="">2012</span> <i title="ACM Press"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/eg5y3lbhlfdsfk6tpvqsesorz4" style="color: black;">Proceedings of the 2nd ACM SIGHIT symposium on International health informatics - IHI &#39;12</a> </i> &nbsp;
• Physio-MIMI: Multi-Modality, Multi-Resource Environment for Physiological and Clinical Research • • Federated data integration environment -Linking existing data resources without a centralized  ...  and Validation of Data Integrity, Process Quality, and Trust • Semantic Provenance Framework addresses three aspects [Prov] o Provenance Modeling o Provenance Query Infrastructure o Scalable  ...  Managing Protected Health Information (PHI) e.g. data encryption "at rest" for RDF store • From retrospective annotation of data (with ontology) to prospective annotation of data: ontology-driven data  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1145/2110363.2110480">doi:10.1145/2110363.2110480</a> <a target="_blank" rel="external noopener" href="https://dblp.org/rec/conf/ihi/SahooSZ12.html">dblp:conf/ihi/SahooSZ12</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/zbh3kd4p4bhn3k5jmu2vjwyfta">fatcat:zbh3kd4p4bhn3k5jmu2vjwyfta</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170810180359/http://cci.case.edu/cci/images/f/fc/SemanticWebinHealthInformatics.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/4d/60/4d60b8dcc60438b1111ad7a2833267183582a048.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1145/2110363.2110480"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> acm.org </button> </a>

Enhancing Clinical Data and Clinical Research Data with Biomedical Ontologies - Insights from the Knowledge Representation Perspective

Jonathan P. Bona, Fred W. Prior, Meredith N. Zozus, Mathias Brochhausen
<span title="2019-08-16">2019</span> <i title="Georg Thieme Verlag KG"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/25ybzim6mvglde3zgjvka7ehii" style="color: black;">IMIA Yearbook of Medical Informatics</a> </i> &nbsp;
We reuse pre-existing ontologies and ensure shared ontological commitment by selecting ontologies from a framework that fosters community-driven collaborative ontology development for biomedicine following  ...  Our aim is to clarify the representational differences between traditional data management and semantic-web-based data management by providing use cases of clinical data and clinical research data re-representation  ...  Nolan assisted with data retrieval and data interpretation in the PRISM research presented in this paper. The authors thank the editors and external reviewers for their valuable input.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1055/s-0039-1677912">doi:10.1055/s-0039-1677912</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/31419826">pmid:31419826</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC6697506/">pmcid:PMC6697506</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/o5pk74rqebhsfhhmt5aems2z2q">fatcat:o5pk74rqebhsfhhmt5aems2z2q</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200710162029/https://www.thieme-connect.com/products/ejournals/pdf/10.1055/s-0039-1677912.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/c6/95/c695a8168ee19c05884f10be1f6a79b780aa4b07.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1055/s-0039-1677912"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> Publisher / doi.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6697506" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Ontology-based Data Integration: A Case Study in Clinical Trials [chapter]

Sandra Geisler, Christoph Quix, Anke Schmeink, David Kensche
<span title="">2010</span> <i title="WORLD SCIENTIFIC"> Science, Engineering, and Biology Informatics </i> &nbsp;
To address the challenges in data management for clinical trials, we developed an ontology-based data integration architecture which is capable of creating executable ETL (Extract-Transform-Load) processes  ...  Furthermore, especially during the development of a medical device the data format may change. Therefore, flexible means to integrate different kinds of data sources and schemas are required.  ...  by the DFG Research Cluster on Ultra High-Speed Mobile Information and Communication UMIC at RWTH Aachen University (http://www.umic.rwth-aachen.de).  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1142/9789814307710_0006">doi:10.1142/9789814307710_0006</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/u2j5lkuwcbhrtazro4aedghfmu">fatcat:u2j5lkuwcbhrtazro4aedghfmu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170830004152/http://dbis.rwth-aachen.de/~quix/papers/DB4LS.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/d5/b6/d5b65677017f8f9c5912f8357d22053c67b83e02.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1142/9789814307710_0006"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> worldscientific.com </button> </a>

A Survey of Ontologies on Disease Classification

<span title="2016-04-05">2016</span> <i title="International Journal of Science and Research"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/odv46yibm5gf7evzoopmrrqr3q" style="color: black;">International Journal of Science and Research (IJSR)</a> </i> &nbsp;
In medical ontology, it is often difficult to establish such definitions for diseases classification. This paper addresses the problem of classifying the disease based on medical ontology.  ...  To evaluate the effectiveness of the intelligent system, three benchmark medical data sets, viz., Breast Cancer Wisconsin, Pima Indians Diabetes, and Liver Disorders from the UCI Repository of Machine  ...  For querying RDF data as well as RDFS and OWL ontologies with knowledge bases, a Simple Protocol and RDF Query Language (SPARQL) is available.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.21275/v5i4.nov162102">doi:10.21275/v5i4.nov162102</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/wjjol3yeljhffmeilxdybk4p7i">fatcat:wjjol3yeljhffmeilxdybk4p7i</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20220309155649/https://www.ijsr.net/archive/v5i4/NOV162102.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/a2/f2/a2f2472a989adb6f93cced7784376ffed56c8ce7.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.21275/v5i4.nov162102"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

Using an integrated ontology and information model for querying and reasoning about phenotypes: The case of autism

Samson W Tu, Samson Tu, Lakshika Tennakoon, Martin O'Connor, Martin Connor, Ravi Shankar, Amar Das
<span title="2008-11-06">2008</span> <i title="American Medical Informatics Association"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/g6q27b56yzeupjryv6lby2r2pa" style="color: black;">AMIA Annual Symposium Proceedings</a> </i> &nbsp;
The Open Biomedical Ontologies (OBO) Foundry is a coordinated community-wide effort to develop ontologies that support the annotation and integration of scientific data.  ...  To enable user queries and inferences about such phenotypes using data in the NDAR repository, we augmented the domain ontology with an information model.  ...  The authors thank Lynn Young, Bill Bug, Dan Hall, and Matt McAulliffe for discussions and assistance on this project and Mor Peleg for her extensive comments.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/18999231">pmid:18999231</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2655950/">pmcid:PMC2655950</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ncuck5asefaklozfupgmye7nzu">fatcat:ncuck5asefaklozfupgmye7nzu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200211131130/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC2655950&amp;blobtype=pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/70/0e/700e4dfbda5353c3651e02573a2f6b910e59e245.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2655950" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

The ACGT Master Ontology and its applications – Towards an ontology-driven cancer research and management system

Mathias Brochhausen, Andrew D. Spear, Cristian Cocos, Gabriele Weiler, Luis Martín, Alberto Anguita, Holger Stenzhorn, Evangelia Daskalaki, Fatima Schera, Ulf Schwarz, Stelios Sfakianakis, Stephan Kiefer (+3 others)
<span title="">2011</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/p4kk6lusgrhyxecgig72iasi5q" style="color: black;">Journal of Biomedical Informatics</a> </i> &nbsp;
This included the careful study of best practices, design principles and evaluation methods for ontology design, maintenance, implementation, and versioning, as well as for use on the part of domain experts  ...  which includes an application updating and evolving the ontology efficiently in response to end-user needs; and (iii) the development of an Ontology-based Trial Management Application (ObTiMA) that integrates  ...  The ACGT project (FP6-2005-IST-026996) is partly funded by the EC and the authors are grateful for this support. The authors thank two anonymous reviewers for valuable comments.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.jbi.2010.04.008">doi:10.1016/j.jbi.2010.04.008</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/20438862">pmid:20438862</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5755590/">pmcid:PMC5755590</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/r5o5r66xazh7dfxh4pfzchb46m">fatcat:r5o5r66xazh7dfxh4pfzchb46m</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190413194441/https://core.ac.uk/download/pdf/82787759.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/ad/46/ad463b0445027903a08bc837a853ecb3baf7f372.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.jbi.2010.04.008"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> elsevier.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5755590" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Ontology driven data integration for autism research

Lynn Young, Samson W. Tu, Lakshika Tennakoon, David Vismer, Vadim Astakhov, Amarnath Gupta, Jeffrey S. Grethe, Maryann E. Martone, Amar K. Das, Matthew J. McAuliffe
<span title="">2009</span> <i title="IEEE"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/qrxicfzd5jcahil6pr67l466ju" style="color: black;">2009 22nd IEEE International Symposium on Computer-Based Medical Systems</a> </i> &nbsp;
The National Database for Autism Research (NDAR) is being constructed to aid in this effort by providing a means for researchers to share and integrate data.  ...  The architecture upon which NDAR is built -the UCSD Developed Data Integration Environment -supports the use of this autism ontology, including annotation of data with ontological concepts and ontology  ...  The core of this environment comprises components for 1) exposing data for federation; 2) mapping data to ontologies; and 3) querying and accessing the data.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1109/cbms.2009.5255362">doi:10.1109/cbms.2009.5255362</a> <a target="_blank" rel="external noopener" href="https://dblp.org/rec/conf/cbms/YoungTTVAGGMDM09.html">dblp:conf/cbms/YoungTTVAGGMDM09</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/eapwzmogyve23l2g2ftjvkovoa">fatcat:eapwzmogyve23l2g2ftjvkovoa</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170808045043/https://www.bioontology.org/sites/default/files/ontology%20driven%20data%20integration.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/d3/3f/d33fc100290e7b8bf2cfc564b83f9798314dfef7.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1109/cbms.2009.5255362"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> ieee.com </button> </a>

HAIKU: A Semantic Framework for Surveillance of Healthcare-Associated Infections

Arash Shaban-Nejad, Alexandre Riazanov, Katia M. Charland, Gregory W. Rose, Christopher J.O. Baker, Robyn Tamblyn, Alan J. Forster, David L. Buckeridge
<span title="2012-08-09">2012</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/cx3f4s3qmfe6bg4qvuy2cxezyu" style="color: black;">Procedia Computer Science</a> </i> &nbsp;
The considerable effort required for discovery and integration of relevant data from multiple sources limits the current effectiveness of HAI surveillance.  ...  The existing terminologies in this domain still suffer from inconsistencies and confusion in different medical/clinical practices, and there is a need for their further improvement and clarification.  ...  We have also explored [7] the possibility of using SADI [8] Semantic Web services for semantic querying of clinical data and reported preliminary progress on prototyping a semantic querying infrastructure  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.procs.2012.06.151">doi:10.1016/j.procs.2012.06.151</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/32288895">pmid:32288895</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC7129430/">pmcid:PMC7129430</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/kyo65lx3effqhf7dbbv32a36bm">fatcat:kyo65lx3effqhf7dbbv32a36bm</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190416080842/https://core.ac.uk/download/pdf/82184044.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/e7/96/e79612f237775d29c1d13750e80abd26d8c84f1c.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.procs.2012.06.151"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> elsevier.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7129430" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

An ontology-guided semantic data integration framework to support integrative data analysis of cancer survival

Hansi Zhang, Yi Guo, Qian Li, Thomas J. George, Elizabeth Shenkman, François Modave, Jiang Bian
<span title="">2018</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/bnylrk2y7bfnrn7u2f2vjkx7ta" style="color: black;">BMC Medical Informatics and Decision Making</a> </i> &nbsp;
the data manipulation and integration processes clearly in the ontologies.  ...  Implemented upon the Ontop platform, we built a data integration pipeline to query, extract, and transform data in relational databases using semantic queries into a pooled dataset according to the downstream  ...  Kama et al. built a Data Definition Ontology (DDO) using the D2RQ (i.e., a platform to provide RDF-based access over relational databases) for accessing heterogeneous clinical data sources [33].  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s12911-018-0636-4">doi:10.1186/s12911-018-0636-4</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/30066664">pmid:30066664</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC6069766/">pmcid:PMC6069766</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/fpazk2lv65b2pargb4qfrll3pi">fatcat:fpazk2lv65b2pargb4qfrll3pi</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190223005044/http://pdfs.semanticscholar.org/3f42/97e1acabb25b9dd96462d8e9adfdca8e2dd7.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/3f/42/3f4297e1acabb25b9dd96462d8e9adfdca8e2dd7.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s12911-018-0636-4"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> springer.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6069766" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Matching Patient Records to Clinical Trials Using Ontologies [chapter]

Chintan Patel, James Cimino, Julian Dolby, Achille Fokoue, Aditya Kalyanpur, Aaron Kershenbaum, Li Ma, Edith Schonberg, Kavitha Srinivas
<span title="">2007</span> <i title="Springer Berlin Heidelberg"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/2w3awgokqne6te4nvlofavy5a4" style="color: black;">Lecture Notes in Computer Science</a> </i> &nbsp;
for clinical trials.  ...  We describe the technical challenges to building a realistic case study, which include problems related to scalability, the integration of large ontologies, and dealing with noisy, inconsistent data.  ...  Acknowledgements We gratefully acknowledge the help that Bishwaranjan Bhattacharjee provided in tuning our database queries.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/978-3-540-76298-0_59">doi:10.1007/978-3-540-76298-0_59</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/sxitrf34anakhajowd4etvammu">fatcat:sxitrf34anakhajowd4etvammu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190504174636/https://link.springer.com/content/pdf/10.1007%2F978-3-540-76298-0_59.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/54/86/548697b3051c61c881940278004c4066c6fa0107.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/978-3-540-76298-0_59"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> springer.com </button> </a>

Clinical Data Integration Model

V. Curcin, A. Barton, M. M. McGilchrist, H. Bastiaens, A. Andreasson, J. Rossiter, L. Zhao, T. N. Arvanitis, A. Taweel, B. C. Delaney, A. Burgun, J. -F. Ethier
<span title="">2015</span> <i title="Schattauer GmbH"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/7rg5h5xpe5fghfe7wwstoiuubm" style="color: black;">Methods of Information in Medicine</a> </i> &nbsp;
Results: The resulting ontology has 549 classes and 82 object properties and is used to support data integration for TRANSFoRm's use cases.  ...  However its use, both in research and clinical work, often requires data from multiple clinical sites, clinical trials databases and registries.  ...  Acknowledgements We would like to thank our colleagues from the TRANSFoRm project for their support and insightful discussions regarding our endeavor.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3414/me13-02-0024">doi:10.3414/me13-02-0024</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/24954896">pmid:24954896</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/2klhhlsebbcnpfc77qtaw7mf4u">fatcat:2klhhlsebbcnpfc77qtaw7mf4u</a> </span>
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